New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
15 months
311
13
163171
0
4
Parser of scientific names !
Dmitry Mozzherin
3 months
24
3
85857
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
2 weeks
26
9
62520
0
12
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
56245
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
5 months
120
50
52793
0
2
Shintaro Katayama
10 months
1
42320
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
3 months
16
1
38996
0
10
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
35502
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
3 years
14
5
33485
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
31357
0
0
Maf parser for BioRuby
Clayton Wheeler
5 years
10
36
28426
0
0
Gff3 parser for big data !
Pjotr Prins
5 years
7
2
26776
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
26245
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 years
3
2
25860
0
17
A biogem to submit jobs on a queue
Francesco Strozzi
5 years
5
...
25176
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
24907
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
2 years
13
3
22750
0
0
Ruby parsering for obo files !
Matt Yoder
6 years
5
...
21755
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
21593
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
18390
0
0
Data mining algorithms for jRuby
arrigonialberto86
4 years
16
3
18365
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
9 weeks
11
5
18159
0
8
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
17201
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
23 months
43
9
14697
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
4 years
14439
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
13995
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
19 months
13598
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
6 years
2
1
13542
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
3 years
3
...
13455
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
13196
0
0
Build genome output files
Michael Barton
4 years
7
...
13091
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
12982
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
8 months
2
...
12737
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
4 years
11
2
12692
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12654
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
today
2
...
12147
4
4
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
11895
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
5 years
2
...
11722
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
6 years
4
...
11575
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
11329
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
19 months
1
...
11195
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
11066
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
2
10977
0
0
Parser to work with file formats used in
Ben J Woodcroft
2 years
...
10875
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
10864
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10255
0
3
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
10001
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
5 years
3
...
9893
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9701
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
9 years
22
1
9678
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8863
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8538
0
0
Ruby binding for samtools tabix
throwern
4 years
5
1
8360
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
8230
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
2 years
8027
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
7945
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
5 years
2
...
7751
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
7 years
12
...
7644
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
20 months
1
...
7628
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
16 months
1
7360
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
3 months
17
4
7308
0
0
Next-generation mapping of mutations
Dan MacLean
5 years
2
...
7203
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
7 years
40
5
7200
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
5 years
13
19
7025
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
4 years
6996
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
4
16
6945
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
6909
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
4 months
...
6870
0
0
Ruby binding to the ucsc kent utilities
throwern
5 years
2
...
6837
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
2 years
1
...
6746
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
2 weeks
1
6524
0
5
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6399
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
6 years
2
1
6370
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
6 years
1
...
6157
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
15 months
1
...
6063
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
4 years
6043
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
5957
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5846
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
6 years
1
...
5500
0
0
A protparam compatible utility for BioRuby
hryk
4 years
2
1
5349
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
5 years
1
...
5310
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5286
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4869
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
5 years
2
...
4738
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4442
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
7 months
6
2
4280
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
2 years
2
1
4230
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
4208
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
24 months
3
...
4034
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
2 years
2
1
3969
0
0
Gggenome Ruby client
Mitsuteru Nakao
4 years
1
...
3796
0
0
Ruby ensembl rest api
Alberto Donizetti
4 years
2
...
3747
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
3 years
6
...
3626
0
0
Generalized linear models for statsample
Ankur Goel
4 years
3613
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
8 years
90
1
3532
0
0
Interface for express beta diversity
Ben J. Woodcroft
3 years
...
3408
0
0
Bio-repeatmasker
Andrei Rozanski
3 years
...
3335
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3325
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
6 years
4
...
3272
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
6 years
3
...
3250
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
3214
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
11 months
3
...
3213
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
6 years
1
3196
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
7 years
1
...
3129
0
0
Web server for bio-samtools
homonecloco
3 years
...
3117
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
3015
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
6 years
1
...
2973
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
6 years
2
...
2965
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
6 years
4
...
2934
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
6 years
...
2922
0
0
One-line summary of your gem
Toshiaki Katayama
6 years
1
...
2921
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
6 years
4
...
2890
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
5 years
1
...
2868
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
6 years
1
...
2857
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2854
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
5 years
1
...
2848
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
5 years
1
...
2833
0
0
Build graph with jRuby
Matteo Picciolini
5 years
2762
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
18 months
...
2620
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
4 years
...
2421
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2270
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2242
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
2204
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2155
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
1950
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1772
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
3 years
1
...
1678
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1633
0
0
Tools to work with fasta files, indexed with
homonecloco
3 years
...
1605
0
0
Tools to manipulate blat files from the command
homonecloco
3 years
...
1568
0
5
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
3 years
...
1534
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1449
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1392
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
8 years
1381
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
2 years
...
1173
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
2 years
1169
0
0
Basic wrapper for the kallistio mapper
homonecloco
2 years
1
...
1145
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
22 months
...
990
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
22 months
...
930
0
0
Biosql plugin for BioRuby
BioRuby project
18 months
...
701
0
0
Cache gemma with loco
Pjotr Prins
3 months
...
547
0
0
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
3 months
...
288
0
6
BioRuby executables: utilities bundled with BioRuby
BioRuby project
3 months
...
277
0
2
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2017-12-15
**) number of commits on GitHub (last 7 days & last 90 days)